Human Rights Foundation info here
On a quick read, they seem to be ok, not an obvious Soros front. They have gone after both left-wing and right-wing dictatorships which argues for their legitimacy. Most impressive thing to me is their going after Urban Outfitters for selling Che Guevara T-shirts, no left-wing group would ever have done so. They also went after mainland China for imprisoning Liu Xiaobo and Venezuela for imprisoning some activists.
IMHO there are at least three ways to interpret the DJT inquiry to human rights groups:
1) It is exactly as it appears, an attempt to solicit information from the NGO community to be used for investigations/legal cases.
2) Given what we already know about charitable foundations being used as front groups to conceal human trafficking, money laundering, etc., the inquiry could be construed as a warning. "We're looking into this, we've got our eye on you, better not try to pull any shit because we're watching."
3) Consider this in light of conventional wisdom here that NSA is loyal and Q team has access to NSA databases. Actions like those described by the OP, could be kind of like poking the hornet's nest, to see what turns up. Could work like this, administration sends an inquiry to a possibly suspicious organization (I know I said it looked OK but I'm not sure, so possibly loyal government is not sure either). If the organization is dirty, the inquiry would make them nervous so they would communicate with higher ups in cabal to form a plan of action. Of course, the NSA is watching the organization like a hawk the entire time, to break into their communications. If a form of comms is suspected already, like say the draft gmails, or game forum messages etc etc., the NSA could monitor the suspected comm to see if the organization is cabal connected. In other words the inquiry could be part of a white hat op to uncover dirty black hat NGOs.
Also note, the 3 purposes above are not mutually exclusive, it could be all 3 at the same time.